SHH1_ARATH
ID SHH1_ARATH Reviewed; 258 AA.
AC Q9XI47; A8MRU8; Q2V4N1; Q8GYR2;
DT 18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=Protein SAWADEE HOMEODOMAIN HOMOLOG 1;
DE AltName: Full=DNA-binding transcription factor 1;
GN Name=SHH1; Synonyms=DTF1; OrderedLocusNames=At1g15215; ORFNames=F9L1.16;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP FUNCTION.
RX PubMed=22064704; DOI=10.1038/cr.2011.173;
RA Liu J., Bai G., Zhang C., Chen W., Zhou J., Zhang S., Chen Q., Deng X.,
RA He X.J., Zhu J.K.;
RT "An atypical component of RNA-directed DNA methylation machinery has both
RT DNA methylation-dependent and -independent roles in locus-specific
RT transcriptional gene silencing.";
RL Cell Res. 21:1691-1700(2011).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, INTERACTION WITH NRPD1, AND
RP DISRUPTION PHENOTYPE.
RX PubMed=21811420; DOI=10.1371/journal.pgen.1002195;
RA Law J.A., Vashisht A.A., Wohlschlegel J.A., Jacobsen S.E.;
RT "SHH1, a homeodomain protein required for DNA methylation, as well as RDR2,
RT RDM4, and chromatin remodeling factors, associate with RNA polymerase IV.";
RL PLoS Genet. 7:E1002195-E1002195(2011).
RN [7]
RP FUNCTION, INTERACTION WITH CLSY1; CLSY2 AND POL IV COMPLEX, DOMAIN, AND
RP MUTAGENESIS OF TYR-140; PHE-162 AND PHE-165.
RX PubMed=23637343; DOI=10.1073/pnas.1300585110;
RA Zhang H., Ma Z.Y., Zeng L., Tanaka K., Zhang C.J., Ma J., Bai G., Wang P.,
RA Zhang S.W., Liu Z.W., Cai T., Tang K., Liu R., Shi X., He X.J., Zhu J.K.;
RT "DTF1 is a core component of RNA-directed DNA methylation and may assist in
RT the recruitment of Pol IV.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:8290-8295(2013).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 125-258 IN COMPLEX WITH HISTONE H3
RP PEPTIDE, FUNCTION, DOMAIN, AND MUTAGENESIS OF GLU-130; TYR-140; ASP-141;
RP PHE-162; PHE-165; CYS-191; TYR-212; HIS-225 AND CYS-232.
RX PubMed=23636332; DOI=10.1038/nature12178;
RA Law J.A., Du J., Hale C.J., Feng S., Krajewski K., Palanca A.M.,
RA Strahl B.D., Patel D.J., Jacobsen S.E.;
RT "Polymerase IV occupancy at RNA-directed DNA methylation sites requires
RT SHH1.";
RL Nature 498:385-389(2013).
CC -!- FUNCTION: Involved in RNA-directed DNA methylation (RdDM). Required for
CC the silencing of some endogenous RdDM targets and accumulation of 24-nt
CC siRNAs, but not for the production of Pol V-dependent transcripts.
CC Functions in transcriptional silencing through both DNA methylation-
CC dependent and -independent pathways. Required for both maintenance and
CC de-novo DNA methylation. Plays a role in the recruitment of Pol IV to
CC genomic regions associated with K9 methylated histone H3 that are
CC targets for RdDM. {ECO:0000269|PubMed:21811420,
CC ECO:0000269|PubMed:22064704, ECO:0000269|PubMed:23636332,
CC ECO:0000269|PubMed:23637343}.
CC -!- SUBUNIT: Associates with the RNA polymerase IV (Pol IV) complex.
CC Interacts with NRPD1, NRPD2, NRPD3, NRPD3B, CLSY1 and CLSY2.
CC {ECO:0000269|PubMed:21811420, ECO:0000269|PubMed:23636332,
CC ECO:0000269|PubMed:23637343}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q9XI47-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9XI47-2; Sequence=VSP_047675;
CC Name=3;
CC IsoId=Q9XI47-3; Sequence=VSP_047674, VSP_047675;
CC -!- DOMAIN: The SAWADEE domain (138-244) binds to mono-, di-, or
CC trimethylated H3K9 histone peptides, but this interaction is impaired
CC if H3K4me2/3 methylation is present (PubMed:23637343 PubMed:23636332).
CC {ECO:0000269|PubMed:23636332, ECO:0000269|PubMed:23637343}.
CC -!- DISRUPTION PHENOTYPE: Loss of DRM2 controlled DNA methylation, but no
CC effect on CMT3 or MET1 controlled methylation.
CC {ECO:0000269|PubMed:21811420}.
CC -!- MISCELLANEOUS: Associates in vivo with Pol IV but not with Pol V
CC (PubMed:23637343) and this interaction is not dependent on its H3K9me
CC binding activity (PubMed:23636332). Glu-130 and Asp-141 interact with
CC the H3K4 side chain while the H3K9me1/2/3 side chains insert into a
CC hydrophobic aromatic cage formed by Tyr-140, Phe-162 and Phe-165
CC (PubMed:23636332). {ECO:0000305|PubMed:23636332,
CC ECO:0000305|PubMed:23637343}.
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DR EMBL; AC007591; AAD39678.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE29286.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE29288.1; -; Genomic_DNA.
DR EMBL; AK117440; BAC42105.1; -; mRNA.
DR EMBL; BT005197; AAO50730.1; -; mRNA.
DR PIR; C86286; C86286.
DR RefSeq; NP_001031048.1; NM_001035971.2. [Q9XI47-2]
DR RefSeq; NP_849666.2; NM_179335.3. [Q9XI47-1]
DR PDB; 4IUP; X-ray; 1.90 A; A/B=125-258.
DR PDB; 4IUQ; X-ray; 2.81 A; A/B=125-258.
DR PDB; 4IUR; X-ray; 2.50 A; A/B=125-258.
DR PDB; 4IUT; X-ray; 2.70 A; A/B=125-258.
DR PDB; 4IUU; X-ray; 2.70 A; A/B=125-258.
DR PDB; 4IUV; X-ray; 2.80 A; A/B=125-258.
DR PDBsum; 4IUP; -.
DR PDBsum; 4IUQ; -.
DR PDBsum; 4IUR; -.
DR PDBsum; 4IUT; -.
DR PDBsum; 4IUU; -.
DR PDBsum; 4IUV; -.
DR AlphaFoldDB; Q9XI47; -.
DR SMR; Q9XI47; -.
DR BioGRID; 23328; 8.
DR STRING; 3702.AT1G15215.2; -.
DR PaxDb; Q9XI47; -.
DR PRIDE; Q9XI47; -.
DR ProteomicsDB; 234503; -. [Q9XI47-1]
DR DNASU; 838088; -.
DR EnsemblPlants; AT1G15215.2; AT1G15215.2; AT1G15215. [Q9XI47-1]
DR EnsemblPlants; AT1G15215.3; AT1G15215.3; AT1G15215. [Q9XI47-2]
DR GeneID; 838088; -.
DR Gramene; AT1G15215.2; AT1G15215.2; AT1G15215. [Q9XI47-1]
DR Gramene; AT1G15215.3; AT1G15215.3; AT1G15215. [Q9XI47-2]
DR KEGG; ath:AT1G15215; -.
DR Araport; AT1G15215; -.
DR TAIR; locus:1005716727; AT1G15215.
DR eggNOG; ENOG502RI2U; Eukaryota.
DR HOGENOM; CLU_053618_0_0_1; -.
DR InParanoid; Q9XI47; -.
DR OMA; TECTCTF; -.
DR PhylomeDB; Q9XI47; -.
DR PRO; PR:Q9XI47; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9XI47; baseline and differential.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003682; F:chromatin binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006306; P:DNA methylation; IMP:TAIR.
DR GO; GO:0006346; P:DNA methylation-dependent heterochromatin assembly; IMP:TAIR.
DR GO; GO:0031047; P:gene silencing by RNA; IMP:TAIR.
DR InterPro; IPR032001; SAWADEE_dom.
DR InterPro; IPR039276; SHH1/2.
DR PANTHER; PTHR33827; PTHR33827; 1.
DR Pfam; PF16719; SAWADEE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Metal-binding; Nucleus;
KW Reference proteome; Zinc.
FT CHAIN 1..258
FT /note="Protein SAWADEE HOMEODOMAIN HOMOLOG 1"
FT /id="PRO_0000423317"
FT REGION 138..244
FT /note="SAWADEE domain"
FT BINDING 191
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 225
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 230
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 232
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT VAR_SEQ 1..21
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:11910074,
FT ECO:0000303|PubMed:14593172"
FT /id="VSP_047674"
FT VAR_SEQ 244..258
FT /note="EESLGLERICRRPEE -> ECMFRNRWD (in isoform 2 and
FT isoform 3)"
FT /evidence="ECO:0000303|PubMed:11910074,
FT ECO:0000303|PubMed:14593172"
FT /id="VSP_047675"
FT MUTAGEN 130
FT /note="E->A: DNA methylation defects."
FT /evidence="ECO:0000269|PubMed:23636332"
FT MUTAGEN 140
FT /note="Y->A: Loss of interaction with H3K9 and DNA
FT methylation defects."
FT /evidence="ECO:0000269|PubMed:23636332,
FT ECO:0000269|PubMed:23637343"
FT MUTAGEN 141
FT /note="D->A: Strong DNA methylation defects."
FT /evidence="ECO:0000269|PubMed:23636332"
FT MUTAGEN 162
FT /note="F->A: Loss of interaction with H3K9 and strong DNA
FT methylation defects, when associated with A-165."
FT /evidence="ECO:0000269|PubMed:23636332,
FT ECO:0000269|PubMed:23637343"
FT MUTAGEN 165
FT /note="F->A: Loss of interaction with H3K9 and strong DNA
FT methylation defects, when associated with A-162."
FT /evidence="ECO:0000269|PubMed:23636332,
FT ECO:0000269|PubMed:23637343"
FT MUTAGEN 191
FT /note="C->A: Decreased stability of the protein."
FT /evidence="ECO:0000269|PubMed:23636332"
FT MUTAGEN 212
FT /note="Y->A: DNA methylation defects."
FT /evidence="ECO:0000269|PubMed:23636332"
FT MUTAGEN 225
FT /note="H->A: Decreased stability of the protein. Decreased
FT stability of the protein; when associated with A-232."
FT /evidence="ECO:0000269|PubMed:23636332"
FT MUTAGEN 232
FT /note="C->A: Decreased stability of the protein; when
FT associated with A-225."
FT /evidence="ECO:0000269|PubMed:23636332"
FT STRAND 129..132
FT /evidence="ECO:0007829|PDB:4IUP"
FT TURN 134..136
FT /evidence="ECO:0007829|PDB:4IUP"
FT STRAND 139..150
FT /evidence="ECO:0007829|PDB:4IUP"
FT STRAND 156..162
FT /evidence="ECO:0007829|PDB:4IUP"
FT HELIX 167..169
FT /evidence="ECO:0007829|PDB:4IUR"
FT STRAND 171..174
FT /evidence="ECO:0007829|PDB:4IUP"
FT HELIX 175..178
FT /evidence="ECO:0007829|PDB:4IUP"
FT STRAND 179..181
FT /evidence="ECO:0007829|PDB:4IUP"
FT HELIX 188..193
FT /evidence="ECO:0007829|PDB:4IUP"
FT STRAND 199..206
FT /evidence="ECO:0007829|PDB:4IUP"
FT STRAND 209..221
FT /evidence="ECO:0007829|PDB:4IUP"
FT STRAND 233..238
FT /evidence="ECO:0007829|PDB:4IUP"
FT TURN 239..241
FT /evidence="ECO:0007829|PDB:4IUP"
FT STRAND 244..247
FT /evidence="ECO:0007829|PDB:4IUP"
FT HELIX 249..251
FT /evidence="ECO:0007829|PDB:4IUP"
FT STRAND 252..254
FT /evidence="ECO:0007829|PDB:4IUP"
SQ SEQUENCE 258 AA; 29506 MW; A4A4F409CEC26DAD CRC64;
MAASDDSSHY FTEFTLSEIV DMENLYKELG DQSLHKDFCQ TVASTFSCSV NRNGKSSITW
KQVQIWFQEK LKHQSQPKSK TLPSPPLQIH DLSNPSSYAS NASNATFVGN STFVQTRKGK
ASDLADLAFE AKSARDYAWY DVSSFLTYRV LRTGELEVRV RFSGFDNRHD EWVNVKTSVR
ERSIPVEPSE CGRVNVGDLL LCFQEREDQA LYCDGHVLNI KRGIHDHARC NCVFLVRYEL
DNTEESLGLE RICRRPEE
